@article{BLAST,
  title={Basic local alignment search tool},
  author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J and others},
  journal={Journal of molecular biology},
  volume={215},
  number={3},
  pages={403--410},
  year={1990},
  publisher={Elsevier Science}
}

@article{garey1976complexity,
  title={The complexity of flowshop and jobshop scheduling},
  author={Garey, Michael R and Johnson, David S and Sethi, Ravi},
  journal={Mathematics of operations research},
  volume={1},
  number={2},
  pages={117--129},
  year={1976},
  publisher={INFORMS}
}

@INPROCEEDINGS{bCloudBLAST,
author={Zhen Meng and Li, Jianhui and Yunchun Zhou and Qi Liu and Yong Liu and Wei Cao},
booktitle={Biomedical Engineering and Informatics (BMEI), 2011 4th International Conference on}, title={bCloudBLAST: An efficient mapreduce program for bioinformatics applications},
year={2011},
volume={4},
pages={2072-2076},
keywords={DNA;Java;Linux;bioinformatics;molecular biophysics;molecular configurations;parallel databases;proteins;query processing;DNA databases;Hadoop libraries;Java;Linux;MapReduce program;NacOS systems;UNIX;Windows;bCloudBLAST;bioinformatics;input query sequence files;parallel implementation;protein databases;sequence databases;sequence similarities;Bioinformatics;Computer architecture;Databases;Phylogeny;Protein sequence;Virtual machining;BLAST;Bioinformatics;Cloud computing;MapReduce;bCloudBLAST},
doi={10.1109/BMEI.2011.6098717},}

@INPROCEEDINGS{Grider:PaScal,
author={Grider, G. and Chen, H. and Nunez, J. and Poole, S. and Wacha, R. and Fields, P. and Martinez, R. and Martinez, P. and Khalsa, S. and Matthews, A. and Gibson, G.},
booktitle={Performance, Computing, and Communications Conference, 2006. IPCCC 2006. 25th IEEE International}, title={PaScal - a new parallel and scalable server IO networking infrastructure for supporting global storage/file systems in large-size Linux clusters},
year={2006},
pages={10 pp.-340},
keywords={IP networks;Linux;file servers;resource allocation;routing protocols;workstation clusters;IO networking infrastructure;IP based global storage system;IPC computing;Linux cluster;PaScal;gigabit Ethernet;global storage-file system;inter-process communication;load balancing;multilevel switch-fabric interconnection network;multipath routing;open-standard IP network;parallel and scalable server;Bandwidth;Communication switching;Computer networks;File servers;File systems;Large-scale systems;Linux;Multiprocessor interconnection networks;Network servers;Routing},
doi={10.1109/.2006.1629424},
}


@inproceedings{Avron:shared-memory,
 author = {Avron, Haim and Gupta, Anshul},
 title = {Managing data-movement for effective shared-memory parallelization of out-of-core sparse solvers},
 booktitle = {Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis},
 series = {SC '12},
 year = {2012},
 isbn = {978-1-4673-0804-5},
 location = {Salt Lake City, Utah},
 pages = {102:1--102:11},
 articleno = {102},
 numpages = {11},
 url = {http://dl.acm.org/citation.cfm?id=2388996.2389134},
 acmid = {2389134},
 publisher = {IEEE Computer Society Press},
 address = {Los Alamitos, CA, USA},
} 

@report{MPI,
author = {},
title = {Message Passing Interface Forum MPI: Message Passing Interface Standard},
type = {•},
institution = {•},
year = {June 1995},
OPTsubtitle = {•},
OPTtitleaddon = {•},
OPTlanguage = {•},
OPTnumber = {•},
OPTversion = {•},
OPTnote = {•},
OPTlocation = {•},
OPTmonth = {•},
OPTisrn = {•},
OPTchapter = {•},
OPTpages = {•},
OPTpagetotal = {•},
OPTaddendum = {•},
OPTpubstate = {•},
OPTdoi = {•},
OPTeprint = {•},
OPTeprintclass = {•},
OPTeprinttype = {•},
OPTurl = {•},
OPTurldate = {•},
}

@article{Ientification,
  title={Ientification of Common Molecular Subsequences},
  author={T. Smith and M. Waterman},
  journal={Journal of molecular biology},
  volume={174},
  number={2},
  pages={195--197},
  year={1881},
  publisher={Elsevier Science}
}

@article{needleman1970general,
  title={A general method applicable to the search for similarities in the amino acid sequence of two proteins},
  author={Needleman, Saul B and Wunsch, Christian D and others},
  journal={Journal of molecular biology},
  volume={48},
  number={3},
  pages={443--453},
  year={1970},
  publisher={Elsevier Science}
}

@article{pearson1988improved,
  title={Improved tools for biological sequence comparison},
  author={Pearson, William R and Lipman, David J},
  journal={Proceedings of the National Academy of Sciences},
  volume={85},
  number={8},
  pages={2444--2448},
  year={1988},
  publisher={National Acad Sciences}
}

@article{mpiBLAST:design,
  title={The design, implementation, and evaluation of mpiBLAST},
  author={Darling, Aaron and Carey, Lucas and Feng, Wu-chun},
  journal={Proceedings of ClusterWorld},
  volume={2003},
  year={2003}
}

@article{BLAST:parallelization,
  title={Parallelization of local BLAST service on workstation clusters},
  author={Braun, RC and Pedretti, Kevin T and Casavant, Thomas L and Scheetz, Todd E and Birkett, CL and Roberts, Chad A},
  journal={Future Generation Computer Systems},
  volume={17},
  number={6},
  pages={745--754},
  year={2001},
  publisher={Elsevier}
}

@article{BLAST:PSI-BLAST,
  title={Gapped BLAST and PSI-BLAST: a new generation of protein database search programs},
  author={Altschul, Stephen F and Madden, Thomas L and Sch{\"a}ffer, Alejandro A and Zhang, Jinghui and Zhang, Zheng and Miller, Webb and Lipman, David J},
  journal={Nucleic acids research},
  volume={25},
  number={17},
  pages={3389--3402},
  year={1997},
  publisher={Oxford Univ Press}
}

@article{Lin:mpiBLAST-pio,
 author = {Lin, Heshan and Ma, Xiaosong and Feng, Wuchun and Samatova, Nagiza F.},
 title = {Coordinating Computation and I/O in Massively Parallel Sequence Search},
 journal = {IEEE Trans. Parallel Distrib. Syst.},
 issue_date = {April 2011},
 volume = {22},
 number = {4},
 month = apr,
 year = {2011},
 issn = {1045-9219},
 pages = {529--543},
 numpages = {15},
 url = {http://dx.doi.org/10.1109/TPDS.2010.101},
 doi = {10.1109/TPDS.2010.101},
 acmid = {1957581},
 publisher = {IEEE Press},
 address = {Piscataway, NJ, USA},
 keywords = {BLAST., Scheduling, Scheduling, parallel I/O, bioinformatics, parallel genomic sequence search, BLAST., bioinformatics, parallel I/O, parallel genomic sequence search},
} 

@ARTICLE{ScalaBLAST,
author={Oehmen, C. and Nieplocha, Jarek},
journal={Parallel and Distributed Systems, IEEE Transactions on}, title={ScalaBLAST: A Scalable Implementation of BLAST for High-Performance Data-Intensive Bioinformatics Analysis},
year={2006},
volume={17},
number={8},
pages={740-749},
keywords={DNA;biology computing;distributed shared memory systems;genetics;proteins;sequences;storage management;very large databases;DNA;ScalaBLAST;bacterial genome;data prefetching;distributed memory;genetic code;high-performance data-intensive bioinformatics analysis;latency hiding;mammalian genome;multilevel parallelism;parallel I/O;protein components;protein information;sequence alignment;sequence matching problem;shared memory architecture;task scheduling;very large databases;Assembly;Bioinformatics;DNA;Data analysis;Databases;Genetics;Genomics;Microorganisms;Proteins;Sequences;BLAST;Global Arrays.;High-performance sequence alignment},
doi={10.1109/TPDS.2006.112},
ISSN={1045-9219},
}

@article{Globalarrays,
year={1996},
issn={0920-8542},
journal={The Journal of Supercomputing},
volume={10},
number={2},
doi={10.1007/BF00130708},
title={Global arrays: A nonuniform memory access programming model for high-performance computers},
url={http://dx.doi.org/10.1007/BF00130708},
publisher={Kluwer Academic Publishers},
keywords={NUMA architecture; parallel programming models; shared memory; parallel programming environments; distributed arrays; global arrays; one-sided communication; scientific computing; Grand Challenges; computational chemistry},
author={Nieplocha, Jaroslaw and Harrison, RobertJ. and Littlefield, RichardJ.},
pages={169-189},
language={English}
}

@inproceedings{ParallelApproach,
 author = {Wu, Changjun and Kalyanaraman, Ananth},
 title = {An efficient parallel approach for identifying protein families in large-scale metagenomic data sets},
 booktitle = {Proceedings of the 2008 ACM/IEEE conference on Supercomputing},
 series = {SC '08},
 year = {2008},
 isbn = {978-1-4244-2835-9},
 location = {Austin, Texas},
 pages = {35:1--35:10},
 articleno = {35},
 numpages = {10},
 url = {http://dl.acm.org/citation.cfm?id=1413370.1413406},
 acmid = {1413406},
 publisher = {IEEE Press},
 address = {Piscataway, NJ, USA},
} 

@inproceedings{NucleotideAlignment,
 author = {Borovska, Plamenka and Gancheva, Veska and Markov, Stoyan},
 title = {Parallel performance evaluation of sequence nucleotide alignment on the supercomputer BlueGene/P},
 booktitle = {Proceedings of the 5th European conference on European computing conference},
 series = {ECC'11},
 year = {2011},
 isbn = {978-960-474-297-4},
 location = {Paris, France},
 pages = {462--467},
 numpages = {6},
 url = {http://dl.acm.org/citation.cfm?id=1991016.1991094},
 acmid = {1991094},
 publisher = {World Scientific and Engineering Academy and Society (WSEAS)},
 address = {Stevens Point, Wisconsin, USA},
 keywords = {biocomputing, high performance computing, human genome, influenza virus, mpiBLAST, parallel performance, sequences alignment},
} 

@inproceedings{In-situProcessing,
 author = {Bennett, Janine C. and Abbasi, Hasan and Bremer, Peer-Timo and Grout, Ray and Gyulassy, Attila and Jin, Tong and Klasky, Scott and Kolla, Hemanth and Parashar, Manish and Pascucci, Valerio and Pebay, Philippe and Thompson, David and Yu, Hongfeng and Zhang, Fan and Chen, Jacqueline},
 title = {Combining in-situ and in-transit processing to enable extreme-scale scientific analysis},
 booktitle = {Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis},
 series = {SC '12},
 year = {2012},
 isbn = {978-1-4673-0804-5},
 location = {Salt Lake City, Utah},
 pages = {49:1--49:9},
 articleno = {49},
 numpages = {9},
 url = {http://dl.acm.org/citation.cfm?id=2388996.2389063},
 acmid = {2389063},
 publisher = {IEEE Computer Society Press},
 address = {Los Alamitos, CA, USA},
} 

@INPROCEEDINGS{DataManagement,
author={Zhang, Zhao and Katz, Daniel S. and Wozniak, Justin M. and Espinosa, Allan and Foster, Ian},
booktitle={High Performance Computing, Networking, Storage and Analysis (SC), 2012 International Conference for}, title={Design and analysis of data management in scalable parallel scripting},
year={2012},
pages={1-11},
keywords={Computer architecture;Computers;Databases;Engines;Optimization;Runtime;Servers},
doi={10.1109/SC.2012.44},
ISSN={2167-4329},}

@INPROCEEDINGS{Wang:VisIO,
author={Mitchell, C. and Ahrens, J. and Jun Wang},
booktitle={Parallel Distributed Processing Symposium (IPDPS), 2011 IEEE International}, title={VisIO: Enabling Interactive Visualization of Ultra-Scale, Time Series Data via High-Bandwidth Distributed I/O Systems},
year={May},
pages={68-79},
keywords={application program interfaces;data visualisation;distributed processing;file organisation;input-output programs;message passing;time series;HDFS;I/O library;I/O subsystem;Lustre installation;MPI file system semantics;N-to-N reads;POSIX file system semantics;TACC Longhorn cluster;VisIO system;data partitioning rules;file formats;global ocean salinity simulation;hadoop distributed file system;high-bandwidth distributed I/O systems;interactive visualization;nonPOSIX distributed file system;parallel enabled readers;petascale simulations;shared-nothing approach;ultra-scale time series data;Computational modeling;Data visualization;Distributed databases;File systems;Libraries;Pipelines;Testing},
doi={10.1109/IPDPS.2011.17},
ISSN={1530-2075},}

@INPROCEEDINGS{CloudBLAST,
author={Matsunaga, A. and Tsugawa, M. and Fortes, J.},
booktitle={eScience, 2008. eScience '08. IEEE Fourth International Conference on}, 
title={CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications},
year={Dec.},
pages={222-229},
keywords={application program interfaces;bioinformatics;message passing;virtual machines;wide area networks;CloudBLAST;MPI-based solution;MapReduce;WAN-based test bed;bioinformatics applications;bioinformatics tool;computing resources;distributed computing;distributed resources;message passing interface;network virtualization;virtual machines;virtual network technology;wide area networks;Application virtualization;Bioinformatics;Computer network management;Distributed computing;Environmental management;Resource management;Resource virtualization;Technology management;Testing;Virtual machining;Cloud computing;bioinformatics;mapreduce;virtualization},
doi={10.1109/eScience.2008.62},}

@INPROCEEDINGS{lin:EfficientDataAccess, 
author={Heshan Lin and Xiaosong Ma and Chandramohan, P. and Geist, A. and Samatova, N.}, 
booktitle={Parallel and Distributed Processing Symposium, 2005. Proceedings. 19th IEEE International}, title={Efficient Data Access for Parallel BLAST}, 
year={April}, 
pages={72b-72b}, 
keywords={biology computing;data handling;message passing;parallel programming;public domain software;query processing;bioinformatics;biological sequence database;biological sequence search application;caching;computation-intensive alignment;computational biology;data access;data handling;data management overhead;database partitioning;mpiBLAST scalability;open-source parallel BLAST tool;optimization;parallel sequence search application;parallel sequence search tool;sequence alignment engine;Bioinformatics;Biology computing;Computational biology;Concurrent computing;Data handling;Databases;Engines;Merging;Sequences;Supercomputers}, 
doi={10.1109/IPDPS.2005.190},}

@INPROCEEDINGS{sequence-searching:ad-hoc,
 author = {Gardner, Mark K. and Feng, Wu-chun and Archuleta, Jeremy and Lin, Heshan and Mal, Xiaosong},
 title = {Parallel genomic sequence-searching on an ad-hoc grid: experiences, lessons learned, and implications},
 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing},
 series = {SC '06},
 year = {2006},
 isbn = {0-7695-2700-0},
 location = {Tampa, Florida},
 articleno = {104},
 url = {http://doi.acm.org/10.1145/1188455.1188564},
 doi = {10.1145/1188455.1188564},
 acmid = {1188564},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {BLAST, agile development, bioinformatics, cluster computing, fault tolerance, grid computing, optical networking, scalability, scheduling, scripting, sequence search},
}
@misc{ref:genedata,
  title     = {1000genomes project},
  howpublished = {http://aws.amazon.com/1000genomes/}
}

@misc{ref:probe,
  title     = {PRObE},
  howpublished = {http://www.nmc-probe.org/}
}

@misc{ref:Marmot,
  title     = {Marmot},
  howpublished = {https://www.nmc-probe.org/wiki/Marmot:Nodes}
}

@misc{ref:fusehdfs,
  title     = {FUSE: Filesystem in Userspace},
  howpublished = {http://fuse.sourceforge.net/}
}

@misc{ref:Genomesproject,
  title     = {Genomes to Life project proposal},
  howpublished = {www.genomes2life.org/SNL-ORNL-GTL-Proposal.doc}
}

@online{Genomesproject,
author = {G. Heffelfinger et al},
title = {Genomes to Life project proposal},
year = {•},
url = {www.genomes2life.org/SNL-ORNL-GTL-Proposal.doc},
OPTsubtitle = {•},
OPTtitleaddon = {•},
OPTlanguage = {•},
OPTversion = {•},
OPTnote = {•},
OPTorganization = {•},
OPTdate = {•},
OPTmonth = {•},
OPTaddendum = {•},
OPTpubstate = {•},
OPTurldate = {•},
}

@inproceedings{Lu:AzureBlast,
 author = {Lu, Wei and Jackson, Jared and Barga, Roger},
 title = {AzureBlast: a case study of developing science applications on the cloud},
 booktitle = {Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing},
 series = {HPDC '10},
 year = {2010},
 isbn = {978-1-60558-942-8},
 location = {Chicago, Illinois},
 pages = {413--420},
 numpages = {8},
 url = {http://doi.acm.org/10.1145/1851476.1851537},
 doi = {10.1145/1851476.1851537},
 acmid = {1851537},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {BLAST, Windows Azure, cloud computing},
} 




